Palmitic acid at high concentration modifies the nanoscale structure of anhydrous milk fat

We performed a nanoscale study based on X-ray scattering to understand the impact of a promotor of crystallization, palmitic acid (PA), at high concentration, on the networks of triacylglycerols (TAGs) in anhydrous milk fat (AMF). Melted blends containing 10 wt% PA were quenched at 25 °C. X-ray scattering data were compared with those obtained for pure AMF, pure PA, and AMF containing 1 wt% PA. While PA at low concentration did not modify the nanostructure of TAG crystals (direct crystallization in the β'-2L form), a high concentration of this promotor favored the formation of polymorphic forms suggesting that PA first crystallizes and then directs crystallization of AMF TAGs towards α and β forms.

Redox-Regulated and Guest-Driven Transformations of Aromatic Oligoamide Foldamers in Advanced Structures

In this study, we demonstrate that an aromatic oligoamide sequence assembles into a trimeric helix-turn-helix architecture with a disulfide linkage, and upon cleavage of this linkage, it reconstructs into an antiparallel double helix. The antiparallel double helix is accessible to encapsulate a diacid guest within its cavity, forming a 2:1 host-guest complex. In contrast, hydrogen-bonding interactions between the trimeric-assembled structure and guests induce a conformational shift in the trimeric helix, resulting in a cross-shaped double-helix complex at a 2:2 host-guest ratio. Interconversions between the trimeric helix and the antiparallel double helix, along with their respective host-guest complexes, can be initiated through thiol/disulfide redox-mediated regulation.

Does Acinetobacter calcoaceticus glucose dehydrogenase produce self-damaging H2O2?

The soluble glucose dehydrogenase (sGDH) from Acinetobacter calcoaceticus has been widely studied and is used, in biosensors, to detect the presence of glucose, taking advantage of its high turnover and insensitivity to molecular oxygen. This approach, however, presents two drawbacks: the enzyme has broad substrate specificity (leading to imprecise blood glucose measurements) and shows instability over time (inferior to other oxidizing glucose enzymes). We report the characterization of two sGDH mutants: the single mutant Y343F, and the double mutant D143E/Y343F. The mutants present enzyme selectivity and specificity of 1.2 (Y343F) and 5.7 (D143E/Y343F) times higher for glucose compared to that of the wild type. Crystallographic experiments, designed to characterise these mutants, surprisingly revealed that the prosthetic group PQQ (pyrroloquinoline quinone), essential for the enzymatic activity, is in a cleaved form for both wild-type and mutant structures. We provide evidence suggesting that the sGDH produces H2O2, the level of production depending on the mutation. In addition, spectroscopic experiments allowed us to follow the self-degradation of the prosthetic group and the disappearance of sGDH's glucose oxidation activity. These studies suggest that the enzyme is sensitive to its self-production of H2O2. We show that the premature aging of sGDH can be slowed down by adding catalase to consume the H2O2 produced, allowing the design of a more stable biosensor over time. Our research opens questions about the mechanism of H2O2 production and the physiological role of this activity by sGDH.

A Chiral [2+3] Covalent Organic Cage Based on 1,1'-Bi-2-naphthol (BINOL) Units

A [2+3] chiral covalent organic cage is produced through a dynamic covalent chemistry approach by mixing two readily available building units, viz. an enantiopure 3,3'-diformyl 2,2'-BINOL compound (A) with a triamino spacer (B). The two enantiomeric (R,R,R) and (S,S,S) forms of the cage C are formed nearly quantitatively thanks to the reversibility of the imine linkage. The X-ray diffraction analysis of cage (S,S,S)-C highlights that the six OH functions of the BINOL fragments are positioned inside the cage cavity. Upon reduction of the imine bonds of cage C, the amine cage D is obtained. The ability of the cage D to host the 1-phenylethylammonium cation (EH+) as a guest is evaluated through UV, CD and DOSY NMR studies. A higher binding constant for (R)-EH+ cation (Ka=1.7 106±10 % M-1) related to (S)-EH+ (Ka=0.9 106±10 % M-1) is determined in the presence of the (R,R,R)-D cage. This enantiopreference is in close agreement with molecular dynamics simulation.

Frequency of an intrathecal IgM synthesis and MRZ reaction in children with MS

BACKGROUND

Multiple sclerosis (MS) is a chronic inflammatory and demyelinating disease of the CNS. An intrathecal IgM synthesis is associated with a more rapid progression of MS and the intrathecal immune response to measles -, rubella -and varicella zoster virus (MRZR) which, if present, increases the likelihood of a diagnosis of MS in adults.

OBJECTIVE

To evaluate the frequency of an intrathecal IgM synthesis and MRZR in children with MS. MethodsChildren with MS and a data set including clinical and treatment history, MRI at onset, in addition to a CSF analysis, and determination of antibody index (AI) of measles, rubella, and zoster antibodies, were eligible. The presence of an intrathecal IgM synthesis and/or a positive MRZ reaction were compared to biomarkers of a more progressive disease course.

RESULTS

In 75 children with MS, OCBs were present in 93.3 %). 49,2 % experienced their first relapse within 6 months. 50.7 % had a total lesion load of more than 10 lesions in the first brain MRI. Spinal lesions were identified in 64 %. 23.5 % had a positive MRZR and 40.3 % an intrathecal IgM synthesis. No significant associations were detected between the presence of an intrathecal IgM synthesis and MRZR and parameters including the relapse rate in the first two years.

CONCLUSION

An intrathecal IgM synthesis and a positive MRZR are found in a subset of MS children but are not associated with markers associated with a poor prognosis.

Hfq C-terminal region forms a β-rich amyloid-like motif without perturbing the N-terminal Sm-like structure

Hfq is a pleitropic actor that serves as stress response and virulence factor in the bacterial cell. To execute its multiple functions, Hfq assembles into symmetric torus-shaped hexamers. Extending outward from the hexameric core, Hfq presents a C-terminal region, described as intrinsically disordered in solution. Many aspects of the role and the structure of this region remain unclear. For instance, in its truncated form it can promote amyloid-like filament assembly. Here, we show that a minimal 11-residue motif at the C-terminal end of Hfq assembles into filaments with amyloid characteristics. Our data suggest that the full-length Hfq in its filamentous state contains a similar molecular fingerprint than that of the short β-strand peptide, and that the Sm-core structure is not affected by filament formation. Hfq proteins might thus co-exist in two forms in vivo, either as isolated, soluble hexamers or as self-assembled hexamers through amyloid-reminiscent interactions, modulating Hfq cellular functions.

Synthesis and Crystallographic Characterization of Helical Hairpin Oligourea Foldamers

Invited for the cover of this issue is the group of Gilles Guichard at the University of Bordeaux. The image depicts sketches and technical drawing tools to illustrate the creation and precise characterization of foldamer tertiary structures. Read the full text of the article at 10.1002/chem.202300087.

Membrane plasticity induced by myo-inositol derived archaeal lipids: chemical synthesis and biophysical characterization

Archaeal membrane lipids have specific structures that allow Archaea to withstand extreme conditions of temperature and pressure. In order to understand the molecular parameters that govern such resistance, the synthesis of 1,2-di-O-phytanyl-sn-glycero-3-phosphoinositol (DoPhPI), an archaeal lipid derived from myo-inositol, is reported. Benzyl protected myo-inositol was first prepared and then transformed to phosphodiester derivatives using a phosphoramidite based-coupling reaction with archaeol. Aqueous dispersions of DoPhPI alone or mixed with DoPhPC can be extruded and form small unilamellar vesicles, as detected by DLS. Neutron, SAXS, and solid-state NMR demonstrated that the water dispersions could form a lamellar phase at room temperature that then evolves into cubic and hexagonal phases with increasing temperature. Phytanyl chains were also found to impart remarkable and nearly constant dynamics to the bilayer over wide temperature ranges. All these new properties of archaeal lipids are proposed as providers of plasticity and thus means for the archaeal membrane to resist extreme conditions.

A pH- and Metal-Actuated Molecular Shuttle in Water

The structure of the Viologen-Phenylene-Imidazole (VPI) guest, previously shown to be bound by cucurbit[7]uril (CB[7]) with binding modes depending on pH and silver ions, has been extended by adding hydrophobic groups on the two extremities of VPI before investigations of CB[7] binding by NMR, ITC, X-ray diffraction, UV-vis and fluorescence spectroscopies. With an imidazole station extended by a naphthalene group (VPI-N), binding modes of CB[7] are similar to those previously observed. However, with the viologen extended by a tolyl group (T-VPI), CB[7] preferentially sits on station T, shuttling between the T and P stations at acid pH or after Ag+ addition. The CB[7]•T-VPI complex thus behaves as a metal-actuated thermodynamic stop-and-go molecular shuttle featured by fast and autonomous ring translocation between two stations and a continuum for fractional station occupancy solely and easily controlled by Ag+ concentration.

Structural polymorphism of the low-complexity C-terminal domain of TDP-43 amyloid aggregates revealed by solid-state NMR

Aberrant aggregation of the transactive response DNA-binding protein (TDP-43) is associated with several lethal neurodegenerative diseases, including amyotrophic lateral sclerosis and frontotemporal dementia. Cytoplasmic neuronal inclusions of TDP-43 are enriched in various fragments of the low-complexity C-terminal domain and are associated with different neurotoxicity. Here we dissect the structural basis of TDP-43 polymorphism using magic-angle spinning solid-state NMR spectroscopy in combination with electron microscopy and Fourier-transform infrared spectroscopy. We demonstrate that various low-complexity C-terminal fragments, namely TDP-13 (TDP-43300–414), TDP-11 (TDP-43300–399), and TDP-10 (TDP-43314–414), adopt distinct polymorphic structures in their amyloid fibrillar state. Our work demonstrates that the removal of less than 10% of the low-complexity sequence at N- and C-termini generates amyloid fibrils with comparable macroscopic features but different local structural arrangement. It highlights that the assembly mechanism of TDP-43, in addition to the aggregation of the hydrophobic region, is also driven by complex interactions involving low-complexity aggregation-prone segments that are a potential source of structural polymorphism.

Synthesis and Crystallographic Characterization of Helical Hairpin Oligourea Foldamers

Oligomers designed to form a helix-turn-helix super-secondary structure have been prepared by covalently bridging aliphatic oligourea foldamer helices with either rigid aromatic or more flexible aliphatic spacers. The relative helix orientation in these dimers has been investigated at high resolution using X-ray diffraction analysis. In several cases, racemic crystallography was used to facilitate crystallization and structure determination. All structures were solved by direct methods. Well-defined parallel helical hairpin motifs were observed in all cases when 4,4'-methylene diphenyl diisocyanate was employed as a dimerizing agent, irrespective of primary sequence and chain length.

Molecular torsion springs: alteration of helix curvature in frustrated tertiary folds

The first abiotic foldamer tertiary structures have been recently reported in the form of aromatic helix-turn-helix motifs based on oligo-quinolinecarboxamides held together by intramolecular hydrogen bonds. Tertiary folds were predicted by computational modelling of the hydrogen-bonding interfaces between helices and later verified by X-ray crystallography. However, the prognosis of how the conformational preference inherent to each helix influences the tertiary structure warranted further investigation. Several new helix-turn-helix sequences were synthesised in which some hydrogen bonds have been removed. Contrary to expectations, this change did not strongly destabilise the tertiary folds. On closer inspection, a new crystal structure revealed that helices adopt their natural curvature when some hydrogen bonds are missing and undergo some spring torsion upon forming the said hydrogen bonds, thus potentially giving rise to a conformational frustration. This phenomenon sheds light on the aggregation behaviour of the helices when they are not linked by a turn unit.

A π-Extended Phenanthrene-Fused Aza[7]helicenium as Novel Chiroptically-Active Architecture in Organic and Aqueous Media

The synthesis and characterization of an original π-extended cationic azahelicene is reported. The phenanthrene-fused aza[7]helicene derivative encompasses a total of ten aromatic fused rings leading to a dissymmetric yet helically...

High-affinity single and double helical pseudofoldaxanes with cationic guests

Two aromatic oligoamides, the 8-residue H8 and 16-residue H16, that adopt stable, cavity-containing helical conformations were examined for their complexation of rodlike dicationic guest, octyl viologen (OV2+) and para-bis(trimethylammonium)benzene (TB2+)....

[3]Foldarotaxane-mediated synthesis of an improbable [2]rotaxane

The wrapping of an aromatic oligoamide helix around an active ester-containing [2]rotaxane enforced the sliding and the sequestration of the surrounding macrocycle around a part of the axle for which it has no formal affinity. The foldamer-mediated compartmentalization of the [2]rotaxane shuttle was subsequently used to prepare an improbable rotaxane.

Self-assembling figure-of-eight and pseudoplectoneme aromatic oligoamide ribbons

Two oligoamide macrocycles composed of eight and twelve 7-amino-8-fluoro-2-quinolinecarboxylic acid monomers were synthesised despite the propensity of their acyclic precursors to fold and self-assemble into double helices. Macrocyclisations were made possible through the transient use of helicity disruptors. The resulting macrocyclic ribbons were found to adopt figure-of-eight and pseudoplectoneme shapes that maintain an ability to self-assemble.

Racemic crystal structures of A-DNA duplexes

Racemic crystallography benefits the identification of a structural form of a DNA sequence that was not previously observed for the enantiopure equivalent.

The ease with which racemic mixtures crystallize compared with the equivalent chiral systems is routinely taken advantage of to produce crystals of small molecules. However, biological macromolecules such as DNA and proteins are naturally chiral, and thus the limited range of chiral space groups available hampers the crystallization of such molecules. Inspiring work over the past 15 years has shown that racemic mixtures of proteins, which were made possible by impressive advances in protein chemical synthesis, can indeed improve the success rate of protein crystallization experiments. More recently, the racemic crystallization approach was extended to include nucleic acids as a possible aid in the determination of enantiopure DNA crystal structures. Here, findings are reported that suggest that the benefits may extend beyond this. Two racemic crystal structures of the DNA sequence d(CCCGGG) are described which were found to fold into A-form DNA. This form differs from the Z-form DNA conformation adopted by the chiral equivalent in the solid state, suggesting that the use of racemates may also favour the emergence of new conformations. Importantly, the racemic mixture forms interactions in the solid state that differ from the chiral equivalent (including the formation of racemic pseudo-helices), suggesting that the use of racemic DNA mixtures could provide new possibilities for the design of precise self-assembled nanomaterials and nanostructures.

Selective and Cooperative Photocycloadditions within Multistranded Aromatic Sheets

A series of aromatic helix-sheet-helix oligoamide foldamers composed of several different photosensitive diazaanthracene units have been designed and synthesized. Molecular objects up to 7 kDa were straightforwardly produced on a 100 mg scale. Nuclear magnetic resonance and crystallographic investigations revealed that helix-sheet-helix architectures can adopt one or two distinct conformations. Sequences composed of an even number of turn units were found to fold in a canonical symmetrical conformation with two helices of identical handedness stacked above and below the sheet segment. Sequences composed of an odd number of turns revealed a coexistence between a canonical fold with helices of opposite handedness and an alternate fold with a twist within the sheet and two helices of identical handedness. The proportions between these species could be manipulated, in some cases quantitatively, being dependent on solvent, temperature, and absolute control of helix handedness. Diazaanthracene units were shown to display distinct reactivity toward [4 + 4] photocycloadditions according to the substituent in position 9. Their organization within the sequences was programmed to allow photoreactions to take place in a specific order. Reaction pathways and kinetics were deciphered and product characterized, demonstrating the possibility to orchestrate successive photoreactions so as to avoid orphan units or to deliberately produce orphan units at precise locations. Strong cooperative effects were observed in which the photoreaction rate was influenced by the presence (or absence) of photoadducts in the structure. Multiple photoreactions within the aromatic sheet eventually lead to structure lengthening and stiffening, locking conformational equilibria. Photoproducts could be thermally reverted.

Hexafluoroisobutylation of Enolates Through a Tandem Elimination/Allylic Shift/Hydrofluorination Reaction

The isobutyl side chain is a highly prevalent hydrophobic group in drugs, and it notably constitutes the side chain of leucine. Its replacement by a hexafluorinated version containing two CF3...

Stable pseudo[3]rotaxanes with strong positive binding cooperativity based on shape-persistent aromatic oligoamide macrocycles

New aromatic oligoamide macrocycles with C₃-symmetry bind a bipyridinium guest (G) to form compact pseudo[3]rotaxanes involving interesting enthalpic and entropic contributions. The observed high stabilities and strong positive binding cooperativity are found in few other host-guest systems.

Bacteria associated with wood tissues of Esca-diseased grapevines: functional diversity and synergy with Fomitiporia mediterranea to degrade wood components

Fungi are considered to cause grapevine trunk diseases such as esca that result in wood degradation. For instance, the basidiomycete Fomitiporia mediterranea (Fmed) is overabundant in white rot, a key type of wood‐necrosis associated with esca. However, many bacteria colonize the grapevine wood too, including the white rot. In this study, we hypothesized that bacteria colonizing grapevine wood interact, possibly synergistically, with Fmed and enhance the fungal ability to degrade wood. We isolated 237 bacterial strains from esca‐affected grapevine wood. Most of them belonged to the families Xanthomonadaceae and Pseudomonadaceae. Some bacterial strains that degrade grapevine‐wood components such as cellulose and hemicellulose did not inhibit Fmed growth in vitro. We proved that the fungal ability to degrade wood can be strongly influenced by bacteria inhabiting the wood. This was shown with a cellulolytic and xylanolytic strain of the Paenibacillus genus, which displays synergistic interaction with Fmed by enhancing the degradation of wood structures. Genome analysis of this Paenibacillus strain revealed several gene clusters such as those involved in the expression of carbohydrate‐active enzymes, xylose utilization and vitamin metabolism. In addition, certain other genetic characteristics of the strain allow it to thrive as an endophyte in grapevine and influence the wood degradation by Fmed. This suggests that there might exist a synergistic interaction between the fungus Fmed and the bacterial strain mentioned above, enhancing grapevine wood degradation. Further step would be to point out its occurrence in mature grapevines to promote esca disease development.

Structures of Pathological and Functional Amyloids and Prions, a Solid-State NMR Perspective

Infectious proteins or prions are a remarkable class of pathogens, where pathogenicity and infectious state correspond to conformational transition of a protein fold. The conformational change translates into the formation by the protein of insoluble amyloid aggregates, associated in humans with various neurodegenerative disorders and systemic protein-deposition diseases. The prion principle, however, is not limited to pathogenicity. While pathological amyloids (and prions) emerge from protein misfolding, a class of functional amyloids has been defined, consisting of amyloid-forming domains under natural selection and with diverse biological roles. Although of great importance, prion amyloid structures remain challenging for conventional structural biology techniques. Solid-state nuclear magnetic resonance (SSNMR) has been preferentially used to investigate these insoluble, morphologically heterogeneous aggregates with poor crystallinity. SSNMR methods have yielded a wealth of knowledge regarding the fundamentals of prion biology and have helped to solve the structures of several prion and prion-like fibrils. Here, we will review pathological and functional amyloid structures and will discuss some of the obtained structural models. We will finish the review with a perspective on integrative approaches combining solid-state NMR, electron paramagnetic resonance and cryo-electron microscopy, which can complement and extend our toolkit to structurally explore various facets of prion biology.

Carbo-mer of Barrelene: A Rigid 3D-Carbon-Expanded Molecular Barrel

After extensive studies of 1D and 2D skeletal carbo-mers based on C₈ π-conjugating dialkynylbutatriene units (DABs: ∼C≡C-(R)C=C=C=C(R)-C≡C∼) bridging sp or sp² centers in carbo-butene, carbo-xylylene or carbo-benzene derivatives, 3D versions are envisaged through carbo-barrelenes and partially reduced derivatives thereof where two or three DAB blades span a bridge between sp³ carbinol vertices or ether thereof. For R=Ph, stable representatives were synthesized through a pivotal [6]pericyclynedione, and extensively characterized by spectroscopic, electrochemical and crystallographic methods. Density functional theory calculations allow detailed analysis of structural and electronic features of the 7 Å high C₂₆ barrel-shaped molecules, and show that they can behave as cages for ionic species. Beyond aesthetical concerns, the results could open prospects of applications in host-guest supramolecular chemistry and single molecule charge transport.

Functionalized 1,8-Diazaiptycenes as Monomers for Aromatic Oligoamide Foldamers

Diversification of the structures and the applications possible for foldamers rely on expansion of the building block library available for their synthesis. In this work, we describe the synthesis of a range of three dimensional heteroaromatic monomers, based on iptycene scaffolds, that are suitable for the synthesis of aromatic oligoamide foldamers. These units can be obtained in gram quantities in up to 80 % yield through [4+2] cycloaddition between diester, diamine, and amino acid derivatives of 1,8-diazaanthracenes and a variety of dienophiles. X-ray structural studies of the monomers and an oligomer show that the new motif orients the two heterocyclic rings and attached groups at an angle of approximately 120° to each other, opening new geometric considerations for the design of this class of foldamer.

Interplay between a Foldamer Helix and a Macrocycle in a Foldarotaxane Architecture

The design and synthesis of a novel rotaxane/foldaxane hybrid architecture is reported. The winding of an aromatic oligoamide helix host around a dumbbell-shaped thread-like guest, or axle, already surrounded by a macrocycle was evidenced by NMR spectroscopy and X-ray crystallography. The process proved to depend on the position of the macrocycle along the axle and the associated steric hindrance. The macrocycle thus behaves as a switchable shield that modulates the affinity of the helix for the axle. Reciprocally, the foldamer helix acts as a supramolecular auxiliary that compartmentalizes the axle. In some cases, the macrocycle is forced to move along the axle to allow the foldamer to reach its best recognition site.

Large-Amplitude Conformational Changes in Self-Assembled Multi-Stranded Aromatic Sheets

The orchestration of ever larger conformational changes is made possible by the development of increasingly complex foldamers. Aromatic sheets, a rare motif in synthetic foldamer structures, have been designed so as to form discrete stacks of intercalated aromatic strands through the self‐assembly of two identical subunits. Ion‐mobility ESI‐MS confirms the formation of compact dimers. X‐ray crystallography reveals the existence of two distinct conformational dimeric states that require large changes to interconvert. Molecular dynamics simulation validates the stability of the two conformations and the possibility of their interconversion.

Sensing a binding event through charge transport variations using an aromatic oligoamide capsule

The selective binding properties of a 13-mer oligoamide foldamer capsule composed of 4 different aromatic subunits are reported. The capsule was designed to recognize dicarboxylic acids through multiple-point interactions owing to a combination of protonation/deprotonation events, H-bonding, and geometrical constraints imparted by the rigidity of the foldamer backbone. Compared to tartaric acid, binding of 2,2-difluorosuccinic acid or 2,2,3,3-tetrafluorosuccinic acid resulted in symmetry breaking due to deprotonation of only one of the two carboxylic acid groups of the encapsulated species as shown by NMR studies in solution and by single-crystal X-ray diffraction in the solid state. An analogous 14-mer foldamer capsule terminated with a thiol anchoring group was used to probe the complexation event in self-assembled monolayers on Au substrates. Ellipsometry and polarization-modulation infrared absorption-reflection spectroscopy studies were consistent with the formation of a single molecule layer of the foldamer capsule oriented vertically with respect to the surface. The latter underwent smooth complexation of 2,2-difluorosuccinic acid with deprotonation of one of the two carboxylic acid groups. A significant (80-fold) difference in the charge transport properties of the monolayer upon encapsulation of the dicarboxylic acid was evidenced from conducting-AFM measurements (S = 1.1 × 10-9 vs. 1.4 × 10-11 ohm-1 for the empty and complexed capsule, respectively). The modulation in conductivity was assigned to protonation of the aromatic foldamer backbone.

Light-mediated chiroptical switching of an achiral foldamer host in presence of a carbohydrate guest

A photoresponsive diarylethene was incorporated in an achiral helical foldamer container. A carbohydrate guest was found to induce opposite handedness upon binding to the open and closed forms of the diarylethene-containing foldamer, thus enabling chiroptical switching of an achiral host mediated by a chiral guest.

Optically Active Perovskite CsPbBr3 Nanocrystals Helically Arranged on Inorganic Silica Nanohelices

Perovskite nanocrystals (PNCs) exhibit excellent absorption and luminescent properties. Inorganic silica right (or left) handed nanohelices are used as chiral templates to induce optically active properties to CsPbBr₃ PNCs grafted on their surfaces. In suspension, PNCs grafted on the nanohelices do not show any detectable chiroptical properties. In contrast, in a dried film state, they show large circular dichroism (CD) and circularly polarized luminescence (CPL) signals with dissymmetric factor up to 6 × 10^-3. Grazing incidence X-ray scattering, tomography, and cryo-electron microscopy (EM) have shown closely and helically packed PNCs on the dried helices and much more loosely organized PNCs on helices in suspension. Simulations based on the coupled dipole method (CDM) demonstrate that the CD comes from the dipolar interaction between PNC assembled into a chiral structure and the CD decreases with the interparticle distance.

Identification of NLR-associated Amyloid Signaling Motifs in Bacterial Genomes

In filamentous fungi, amyloid signaling sequences allow Nod-like receptors (NLRs) to activate downstream cell-death inducing proteins with HeLo and HeLo-like (HELL) domains and amyloid RHIM and RHIM-related motifs control immune defense pathways in mammals and flies. Herein, we show bioinformatically that analogous amyloid signaling motifs exist in bacteria. These short motifs are found at the N terminus of NLRs and at the C terminus of proteins with a domain we term BELL. The corresponding NLR and BELL proteins are encoded by adjacent genes. We identify 10 families of such bacterial amyloid signaling sequences (BASS), one of which (BASS3) is homologous to RHIM and a fungal amyloid motif termed PP. BASS motifs occur nearly exclusively in bacteria forming multicellular structures (mainly in Actinobacteria and Cyanobacteria). We analyze experimentally a subset of seven of these motifs (from the most common BASS1 family and the RHIM-related BASS3 family) and find that these sequences form fibrils in vitro. Using a fungal in vivo model, we show that all tested BASS-motifs form prions and that the NLR-side motifs seed prion-formation of the corresponding BELL-side motif. We find that BASS3 motifs show partial prion cross-seeding with mammalian RHIM and fungal PP-motifs and that proline mutations on key positions of the BASS3 core motif, conserved in RHIM and PP-motifs, abolish prion formation. This work expands the paradigm of prion amyloid signaling to multicellular prokaryotes and suggests a long-term evolutionary conservation of these motifs from bacteria, to fungi and animals.

Aromatic foldamers as scaffolds for metal second coordination sphere design

As metalloproteins exemplify, the chemical and physical properties of metal centers depend not only on their first but also on their second coordination sphere. Installing arrays of functional groups around the first coordination sphere of synthetic metal complexes is thus highly desirable, but it remains a challenging objective. Here we introduce a novel approach to produce tailored second coordination spheres. We used bioinspired artificial architectures based on aromatic oligoamide foldamers to construct a rigid, modular and well-defined environment around a metal complex. Specifically, aza-aromatic monomers having a tethered [2Fe-2S] cluster have been synthesized and incorporated in conical helical foldamer sequences. Exploiting the modularity and predictability of aromatic oligoamide structures allowed for the straightforward design of a conical architecture able to sequester the metal complex in a confined environment. Even though no direct metal complex-foldamer interactions were purposely designed in this first generation model, crystallography, NMR and IR spectroscopy concurred to show that the aromatic oligoamide backbone alters the structure and fluxional processes of the metal cluster.

Multiturn Hollow Helices: Synthesis and Folding of Long Aromatic Oligoamides

Aromatic oligoamides adopting helical conformations are synthesized by coupling carboxyl-terminated basic units having two, four, and eight residues to amine-terminated oligomer precursors. Coupling yields show no noticeable reduction with the size of the basic units or the final product. One- and two-dimensional NMR spectroscopy and computational studies demonstrate the reliable helical folding of these oligomers. The X-ray structure of 16mer 7 reveals a compact, multiturn helix having a 9 Å inner pore.

Hybrid Sequences that Express both Aromatic Amide and α-Peptidic Folding Features

Foldamers combining aliphatic and aromatic main-chain units often produce atypical structures that cannot easily be accessed from purely aromatic or aliphatic sequences. We report solid-state evidence that sequences comprising α-amino acids and quinoline-based monomers adopt conformations that combine the folding propensities of both components. Foldamers 2 and 3 having an XQQ repeat motif (X=α-amino acid, Q=quinoline) were synthesized. Crystals of 2 (X=Phe, Q with an anionic side chain) obtained from water revealed an aromatic helix where amide groups belonging to the α-amino acids created a hydrogen-bond array typical of peptidic helices. Crystals of 3 (X=Ser, Q with a lipophilic side chain) obtained from organic solvents revealed a helix-turn-helix structure in which α-amino acid side chains interfere with main-chain hydrogen bonding. High sequence-dependency of the conformation is typical of peptides but is shown here to include aromatic folding features.

Five-component, one-pot synthesis of an electroactive rotaxane comprising a bisferrocene macrocycle

The templated clipping of a ferrocene-grafted isophthalic acid derivative to encircle a hydrogen-bonding axle through the reaction with 1,4-bis(aminomethyl)benzene is described. The constituent electroactive macrocycle of the resultant [2]rotaxane is a homologue of the versatile benchmark tetraamide variant developed by Leigh and co-workers. The relative templating effect of different hydrogen-bonding motifs in rotaxane and pseudorotaxane generation is compared, with yields varying from 0 to 41%. The electrochemical properties and single crystal X-ray structure of a doubly ferrocene-decorated [2]rotaxane are further reported.

Allosteric Recognition of Homomeric and Heteromeric Pairs of Monosaccharides by a Foldamer Capsule

The recognition of either homomeric or heteromeric pairs of pentoses in an aromatic oligoamide double helical foldamer capsule was evidenced by circular dichroism (CD), NMR spectroscopy, and X-ray crystallography. The cavity of the host was predicted to be large enough to accommodate simultaneously two xylose molecules and to form a 1:2 complex (one container, two saccharides). Solution and solid-state data revealed the selective recognition of the α-4 C1 -d-xylopyranose tautomer, which is bound at two identical sites in the foldamer cavity. A step further was achieved by sequestering a heteromeric pair of pentoses, that is, one molecule of α-4 C1 -d-xylopyranose and one molecule of β-1 C4 -d-arabinopyranose despite the symmetrical nature of the host and despite the similarity of the guests. Subtle induced-fit and allosteric effects are responsible for the outstanding selectivities observed.

Mechanism of Reconstitution/Activation of the Soluble PQQ-Dependent Glucose Dehydrogenase from Acinetobacter calcoaceticus: A Comprehensive Study

The ability to switch on the activity of an enzyme through its spontaneous reconstitution has proven to be a valuable tool in fundamental studies of enzyme structure/reactivity relationships or in the design of artificial signal transduction systems in bioelectronics, synthetic biology, or bioanalytical applications. In particular, those based on the spontaneous reconstitution/activation of the apo-PQQ-dependent soluble glucose dehydrogenase (sGDH) from Acinetobacter calcoaceticus were widely developed. However, the reconstitution mechanism of sGDH with its two cofactors, i.e., pyrroloquinoline quinone (PQQ) and Ca²⁺, remains unknown. The objective here is to elucidate this mechanism by stopped-flow kinetics under single-turnover conditions. The reconstitution of sGDH exhibited biphasic kinetics, characteristic of a square reaction scheme associated with two activation pathways. From a complete kinetic analysis, we were able to fully predict the reconstitution dynamics and also to demonstrate that when PQQ first binds to apo-sGDH, it strongly impedes the access of Ca²⁺ to its enclosed position at the bottom of the enzyme binding site, thereby greatly slowing down the reconstitution rate of sGDH. This slow calcium insertion may purposely be accelerated by providing more flexibility to the Ca²⁺ binding loop through the specific mutation of the calcium-coordinating P248 proline residue, reducing thus the kinetic barrier to calcium ion insertion. The dynamic nature of the reconstitution process is also supported by the observation of a clear loop shift and a reorganization of the hydrogen-bonding network and van der Waals interactions observed in both active sites of the apo and holo forms, a structural change modulation that was revealed from the refined X-ray structure of apo-sGDH (PDB: 5MIN).

Absolute handedness control of oligoamide double helices by chiral oxazolylaniline induction

Aromatic oligoamide double helices bearing a chiral oxazolylaniline moiety were synthesized and their helix handedness was completely controlled (de > 99%).

Structural dissection of amyloid aggregates of TDP-43 and its C-terminal fragments TDP-35 and TDP-16

The TAR DNA-binding protein (TDP-43) self-assembles into prion-like aggregates considered to be the structural hallmark of amyotrophic lateral sclerosis and frontotemporal dementia. Here, we use a combination of electron microscopy, X-ray fiber diffraction, Fourier-transform infrared spectroscopy analysis, and solid-state NMR spectroscopy to investigate the molecular organization of different TDP constructs, namely the full-length TDP-43 (1-414), two C-terminal fragments [TDP-35 (90-414) and TDP-16 (267-414)], and a C-terminal truncated fragment (TDP-43 ∆GaroS2), in their fibrillar state. Although the different protein constructs exhibit similar fibril morphology and a typical cross-β signature by X-ray diffraction, solid-state NMR indicates that TDP-43 and TDP-35 share the same polymorphic molecular structure, while TDP-16 encompasses a well-ordered amyloid core. We identified several residues in the so-called C-terminal GaroS2 (368-414) domain that participates in the rigid core of TDP-16 fibrils, underlining its importance during the aggregation process. Our findings demonstrate that C-terminal fragments can adopt a different molecular conformation in isolation or in the context of the full-length assembly, suggesting that the N-terminal domain and RRM domains play an important role in the TDP-43 amyloid transition.